The Kill Switch and the Key shut the bike down at
EXACTLY THE SAME node.
They are directly in series with each other.
The suggestion that shutting off with the Kill can cause damage to ECU is simply nonsense.
There is a
CAUTION (and it is simply that - not a
'Warning' nor a direct prohibition) against using the Kill in the owner's manual simply because it is easy to forget that you must still turn off the Key to additionally turn off the lighting & ancillary circuits.
This is cut straight out of the owners manual... I to have learnt something from this thread as i have always used the kill switch then stand then key.... This forum is great for learning from the small things like this through to engine removal etc. I'm glad to be a part of it.....
Caution
The engine should normally be stopped by turning the ignition switch to the OFF position. The engine stop switch is for emergency use only. Do not leave the ignition switched on with the engine stopped. Electrical damage may result.
It is a caution against
leaving the key switched on - that & only that! The implied potential 'electrical damage' would be as result of killing the battery.
i.e. the Key has three parallel circuits - ignition, Lighting and Ancillaries (Brake/Turns/Horn)
The Kill obviously only goes to the ignition system - but is connected directly off the output of the Ignition Pole of the Key-Switch.
On my KeyLess it actually breaks both simultaneously*

*(well in truth the Kill output is 0.5 sec ahead of the main power circuit into it because I purposely built in an added time delay for the latch to drop, for additional safety)